Some of the most obvious differences are the rules for the monks. In vajrayana once you reach a certain state of enlightenment or convince your followers, you've reached a certain state. You essentially can do whatever you want and claim it's for the benefit of the students. In the pali canon, an arahat would follow the same rules as a monk who had been ordained for one day. Which would be no inconvenience to them, because there would be no desire to break any of the rules. Which is a direct contradiction. In vajarayana, a monk could have sex with his student as a means of helping them. According to the historical Buddha, that person is immediately no longer a monk. They essentially dismiss the entire pali canon as a lower teaching.
They also think that personal enlightenment/arahatship is a bad thing and that you should keep being reborn to help others. There are entire books written about why that doesn't make sense, but it's against the entire purpose of what the Buddha taught.
There are also a lot of teachings about the self that are categorically listed as wrong view in the pali canon.
I don't want to come of like I'm hating on the school or anyone who practices in it, but it's far from 'Buddhism' in a historical context. There are still many wise and compassionate people who have dedicated their lives to it.